John Shepard: Vol 1
by WolfNinja0303
Summary: John Shepard must save the galaxy all the while dealing with his past, and the mysteries that are his parents past that he can never share with anyone...right?
1. Past, Present, Future

"Shepard…..Shepard...SHEPARD!", Johnathan Shepard snaps back into reality and realizes that he's sitting in the mess hall of the Normandy SR-1. He turns his head to see David Anderson standing over him giving him a look that would have most civilians start sweating nervously, but after being practically raised by the man John has become numb to it. "Are you just going to nap all day or are you going to get ready for the mission?", Anderson asks with a slightly annoyed tone, but John speaks Anderson, he was just being the worried old man he was when John first met him.

"Yes sir just taking a nap.", John dismissed, but Anderson countered, "Has 'just taking a nap' evolved to thrashing with the occasional grunt?", "Well didn't humans evolve from primates is it hard to believe that naps evolved too? The nap evolution is at hand!", Johns voice was laced with obvious sarcasm. However Anderson was in no mood for it, "Commander Johnathan Shepard are you fit for duty?", ' _He's using both my rank and full name he's in full dad mode right now.'_ , "Yes sir, I'll go get my armor."

John leaves for the armory, and on his way out the mess hall he received a few judging and worried looks from the rest of the crew. John never really understood why people couldn't mind their own business. It was one thing for Anderson to be worried, but he was just being daddy Anderson, and to have all these strangers look at him like he was todays' gossip would piss teenage John off. However Anderson has taught him better, and he will ignore them….the best he can.

Later

"I hate that guy" Joker says the moment Nihlus is out of earshot. "Nihlus gave you a compliment… so you hate him?", Kaidan adds. John was in the cockpit with Joker and Kaidan when they went through the Mass Relay he listens to Jokers honest opinions with Kaidans' consistent comments. "You remember to zip up your jumpsuit on the way to the bathroom? That's good. I just jumped us halfway across the galaxy and hit a target the size of a pinhead. So that's incredible! Besides, Spectres are trouble. I don't like having him on board. Call me paranoid.", "Your paranoid. The Council helped fund this project. They have a right to send someone to keep an eye on their investment.", ' _And there's Kaidan obeying every higher up without question like always.'_ , "Yeah, that is the official story. But only an idiot believes the official story.", "You always expect the worst." John adds. "Well bad feelings are an occupational hazard. We don't go anywhere unless there's a good reason, so what are we doing here?" Before John could comment Jokers comm-link went off. " **Joker! Status Report."**

 **In the Comm-Room**

"Commander Shepard. I was hoping you'd get here first. It will give us a chance to talk." When John entered the Comm Room instead of Anderson there was Nihlus. ' _Not the person I'm looking for, but I have to play nice I guess.'_ , "The captain said he'd meet me here." "He's on his way." Nihlus paused looking thoughtful then spoke again, "I'm interested in this world we're going to - Eden Prime. I've heard it's quite beautiful." "I've never been there." "But you know of it. It's become something of a symbol for you people, hasn't it?" ' _That doesn't mean I know anything about it.'_ "Proof that not only humanity can not only establish colonies across the galaxy, but also protect them. But how safe is it really?" ' _Got something to say buddy?'_ "If you've got something to say, just say it." John snapped. "You're people are still newcomers, Shepard. The galaxy can be a very dangerous place." ' _As long as there are people like you.'_ "Is the Alliance truly ready for this?" ' _How dare-"_ Johns thoughts are interupted by Anderson walking into the room.

"I think it's about time we told the commander what's really going on." Just by looking at Anderson, John can tell that he knows that he just walked in on something. But he was kinda glad Anderson did walk in at that moment, that 'nap' earlier still had him on edge, and who knows how many more comments from Nihlus he could take. "This mission is far more than a simple shake down." Nihlus adds. ' _Ffff… I hate it when Joker is right.'_ "Is someone going to fill me in, Captain?" The word 'please' was on Johns tongue, but he knows that he does not need to say it for Anderson to answer. "We're making a covert pick-up on Eden Prime. That's why we needed the stealth systems operational." "There must be a reason you didn't tell me about this sir." "This comes down from the top, Commander. Information strictly on a need-to-know basis." ' _Good, because being leader of the ground team I need to know, and it would've been nice to know earlier!'_

"A research team on Eden Prime unearthed some kind of beacon during an excavation. It was Prothean." ' _That explains Nihlus.'_ " I thought the Protheans vanished 50,000 years ago." Nihlus then decides to bestow his 'wisdom' upon him. " Their legacy still remains. The mass relays, the Citadel, our ship drives - it's all based on Prothean technology." "This is big Shepard. The last time humanity made a discovery like this, it jumped our technology forward two hundred years. But Eden Prime doesn't have the facilities to handle something like this. We need to bring the beacon back to the Citadel for proper study." ' _We get to meet the council. Yay.'_ , "Obviously, this goes beyond mere human interests, Commander. This discovery could affect every species in Council space." ' _I've got nothing against other species, but 'mere human interests?'_ "Why didn't we keep the beacon for ourselves?" "You humans don't have the best reputation. Some species see you as selfish-" ' _Including yours.'_ "Too unpredictable. Too independent. Even dangerous." "Sharing that beacon will improve relations with the Council. Plus we need their scientific expertise. They know more about the Protheans than we do." Like always Anderson has a good point humans need to get off their asses and do something to make others think we want to be treated like equals like we did in the past hopefully it will not end as badly and start another Civil War, but interstellar.

"The beacon is not the only reason I'm here, Shepard." ' _Oh, really?'_ John was genuinely surprised, if the Council didn't just send Nihlus for the Prothean beacon then what else is there for the Council to be interested in? "NIhlus wants to see you in action Commander. He's here to evaluate you." ' _Evaluate? For what?!'_ "What's going on Captain?" "The Alliance has been pushing for this for a long time." ' _Which thing there are quite a few.'_ "Humanity wants a bigger role in shaping interstellar policy. We want more say with the Citadel Council. The Spectres represent the Councils power and authority, if they accept a human into their ranks, it will show how far the alliance has come." ' _Wait. THE SPECTRES!'_ Before Shepard could speak Nihlus entered the conversation again."Not many could've survived what you went through on Akuze. You showed a remarkable will to live - a particularly useful talent. That's why I put your name forward as a candidate for the Spectres." ' _Nihlus put my name forward?! I did not expect THAT! Did I misjudge him?'_

Shepard had to be sure, "Why would a turian want a human for the Spectres?" Not all turians resent humanity. Some of us see the potential of your success. We see what you have to offer to the rest of the galaxy - and the Spectres." Nihlus had once again surprised Shepard, perhaps he really did misjudge him. "We are an elite group. It's rare to find an individual with the skills we seek. I don't care that you're human, Shepard. I only care that you can do the job" ' _This will be an interesting experience.'_ "Just tell me what I have to do." " I need to see your skills for myself, Commander. Eden Prime will be the first of several missions together." Nihlus couldn't see it, but Shepard notices a look in Anderson's eyes it was a look a proud father would give to his son when they had taken the next step in their life. It's a look that he remembers his father giving him many years ago. He wonders what his mother would think, she had only been in the Alliance for a few years before she met his father. Then one day she had to leave for both her sake and his dads'. He then wonders if perhaps if she hadn't met his dad if she would be on this ship with a Spectre candidacy. She wouldn't have been on Mindoir. Maybe she'd still be- ' _No Shepard! What happened, happened. She made her choice, and she lived a good life, maybe not the long one she deserved, but it was enough.'_

For the second time that day Anderson snapped him back into reality, "You'll be in charge of the ground team. Secure the beacon and get it on the ships ASAP. Nihlus will accompany you to observe the mission." Shepard asked a few more questions about the Protheans, Eden Prime, and the beacon then Anderson decided it was time to get going." We should be getting close to Eden-" Anderson was suddenly interrupted by Joker.

" **Captain. We've got a problem."**

A/N: To anyone who even reads these things I am of course WolfNinja0303, and this is my first FanFiction though some of you might be thinking I'm just making a Fanfiction about Shepards' perspective in the game. Do not fret fellow fans this series will have a bit more than that including a bit more insight of my version of Johns backstory, and family, and there will be more characters to add. You will probably be confused, but some of you probably won't. There will be flashbacks so there will be clear stories on how John Shepard became Commander John Shepard, but seriously please just stick with me. Please tell me if my paragraphing is too messy, than perhaps I will learn from my mistakes.

Sneak peaks not really needed for next chapter I think we all know what happens on Eden Prime unless you didn't play the first game and your a Non-Mass Effect Fan in which WHAT ARE YOU DOING HERE?!PLAY THE GAMES!

Anyways see ya'll next time. w


	2. Eden Prime

John could never forget that fateful night.

The night the Batarians came.

The night he watched everything he knew burn.

The night his childhood ended.

Everyone knew that night by one name.

The Raid of Mindoir.

John remembers being a teenager frozen in his hiding place watching everyone scream, run, fall, die, or be dragged away to a fate worst than death. Some people he knew, some he didn't, but watching it all he wished he got the chance to know them. However, out of all of those people he saw that night.

None of them were his parents.

Where are they?

"Your team's the muscle in this operation, Commander. Go in heavy and head straight for the dig sight."

For the first time since he met Anderson, Shepard wasn't listening to the man. He was thinking about Eden Prime. Not the research team, not the artifact, but the people - the citizens. From what he learned from Jenkins this world is nothing but a farm world. So much like his. He thinks of the families. The children that are hiding just as scared as he was. Once again he couldn't do anything about it he was too far from the residential area of the planet. That fact gives him hope that the citizens are far from harms way.

"What about survivors, Captain?" Jenkins asks. ' _Oh right. Jenkins is from this world. How he must feel right now is hard to think about. I should keep an eye out for surviors for his sake.' Anderson states,_ "Helping survivors is a secondary objective. The beacon's your top priority." ' _Is that right?'_

" **Approaching drop point one."**

"Nihlus? You coming with us?" It wasn't until Jenkins said that, that Shepard finally remembered Nihlus was with them. "I move faster on my own." Then Nihlus ran of the ship into the unknown. ' _Well so much for 'This will be the first of several mission together. No just… go ahead. Without back up.'_ Anderson continued with his debrief. "Nihlus will scout out ahead. He'll feed you status reports throughout the mission, otherwise, I want radio silence." "We've got his back, Captain" Shepard reassured. ' _It''ll be hard though, because well you know. We can't exactly see it.'_ "The mission's yours now, Shepard. Good luck."

" **We are approaching drop point two"**

The ship touched down somewhere away from where Nihlus was dropped off. It was near a cliffs edge with a view of the sunset. When the ship left, Shepard, Kaidan, and Jenkins left to find the beacon. Nihlus was suddenly on the radio " **This place got hit hard, Commander. Hostiles everywhere. Keep your guard up."**

The only beautiful thing about Eden Prime right now was the sunset, but besides that everything else looked horrible. And Shepard had agreed when Kaidan pointed out that everything smelled like smoke and death.

Like Mindoir.

Shepard immediately shook that thought from his head, and continued onward. Further onto the trail he hears something. He pulled out his rifle and silently ordered for Kaidan and Jenkins to do the same. He motioned Jenkins forward then he went, and as soon as they did, drones started shooting, hitting Jenkins. Shepard then raced out and shot them all down. After the drones were down Kaidan rushed to Jenkins, Shepard not far behind, only to discover Jenkins was dead. Kaidan kneeled down and closed Jenkins eyes, and slowly got back up. "Ripped right through his shields. Never had a chance." Kaidan said with a solemn voice. "We'll see he receives a proper service once the mission is complete. But I need you stay focused." For a moment Kaidan looked back at Jenkins, but then looked back at Shepard. "Aye, aye, sir."

Shepard felt like he didn't say enough. Like he didn't do enough. However he just tells himself there's nothing else to do or say. ' _At least Jenkins is on his home planet.'_

The ground team, or what's left of it moves on to the trail hoping to avoid death, but being soldiers they know it's inevitable. Suddenly they heard a familiar sound, gun fire. They run toward the source of the sound to find what must have been a survivor in Alliance armor. The woman was taking cover from - ' _The GETH! What are they doing here!'_ The question no longer mattered, for they needed to help their new comrade.

After the geth were down the woman had stepped from cover. "Thanks for your help Commander. I didn't think I was going to make it. Gunnery Chief Williams of the 212. You the one in charge here, sir?" Shepard nods, "Are you wounded Williams?" "A few scrapes and burns. Nothing serious. The others weren't so lucky." Williams had looked sad and ashamed saying that. Shepard of course new that look. It was the same one he had after Akuze. "Oh, man - We were patrolling the perimeter when the attack hit. We tried to get off a distress signal, but they cut off the communications. I've been fighting for my life ever since." ' _Is she the only one left?'_ "Where's the rest of your squad?" "We tried to double back to the beacon. But we walked into ambush" she looked at the ground for a moment "I don't think any of the others… I think I'm the only one left."

"This isn't your fault, Williams. You couldn't have done anything to save them." Shepard hoped it was enough, but from personal experience he knew it wasn't. "Yes, sir. We held our position as long as we could. Until the geth overwhelmed us." Kaidan then said what everyone was thinking. "The geth hasn't been seen outside the Veil in nearly 200 years. Why are they here now?" _'_ _Good question Alenko.'_ "They must have come for the beacon." As good of an accusation that was, the question that was on Shepard's mind now is, why? He knew why the beacon was important to everyone else, but what use did the geth have for it? "The dig site is close. Just over that rise. It might still be there." "We could use your help Williams." Shepard offered. "Aye, aye, sir. It's time for payback." "Move out!"

When they reached the dig site there were more geth surrounding where the beacon should been. After the fight is over they all go toward where the beacon was last. Ashley was the first to say something "This is the dig site. The beacon was right here. It must've been moved." Kaidan interjected "By who? Our side? Or the geth?" "Hard to say. Maybe we'll know more after we check out the research camp." Shepard looks around "You think anyone got out of here alive?" Ashley takes a look around too. "If they were lucky. Maybe hiding up in the camp. It's just at the top of this ridge. Up the ramps." In the first time in a while Nihlus reported in **"Change of plans, Shepard. There's a small spaceport up ahead. I want to check it out. I'll wait for you there."**

The trio left the abandoned dig site, and went up to the camp to see that it was badly hit already. Kaidan cautioned "It's a good place for an ambush. Keep your guard up." At the camp there were spikes with what looked like people or what used to be people, but they were... different. All of a sudden one of them moved and the spike it was impaled on started moving toward the ground as if to let the... thing down. Kaidan cried "Oh god! They're still alive!" "What did the geth do to them?" Ashley asked. Then all they could do was fight the things.

Desperate to find survivors Shepard started with the locked sheds. After unlocking one he found survivors a woman came forward "Humans! Thank the Maker!" There was man limping toward them "Hurry! Close the door! Before the come back!" Shepard got to questions "How did you end up in this shed?" The woman decided to answer "We hid here during the attack. They must have come here for the beacon. Luckily, it wasn't here. It was moved to the spaceport earlier this morning. Manuel and I stayed behind to pack up the camp. When the attack came, the marines held them off long enough for us to hide. They gave their lives to save us." Manuel started to speak like a some mad prophesier "No one was saved. The age of humanity is ended. Soon only ruin and corpses will remain." Shepard needed to know if Nihlus made it to the spaceport "Did you notice a turian in the area?" Manuel answered "I saw him. The prophet. Leader of the enemy. He was here, before the attack." _'What?'_ Kaidan came to the same conclusion "That's impossible. Nihlus was with us on the Normandy before the attack. He couldn't have been here." "I'm sorry. Manuel's still a bit... unsettled. We haven't seen your turian. We've been hiding here since the attack." Shepard asked what the scientist knew about the beacon and other question with her assistant sometimes interrupting. Shepard knew enough, "Williams, lead us to the spaceport." "You can't stop it. Nobody can stop it. Night is falling. The darkness of eternity." Manuel warned them again only for Dr. Warren to attempt to calm him down. "Hush, Manuel. Go lie down. You'll feel better once the medication kicks in."

The team left the camp and made their way toward the spaceport only to hear the sound of a single gunshot coming from the direction of the spaceport. _'Nihlus!'_ They started to across the little distance left between them and the spaceport. Then they saw it. "What is that!? Off in the distance." Kaidan exclaimed. "It's a ship. Look a the size of it!" Ashley answered. The 'ship' was humongous it looked like a squid with arms smaller then the body. Shepard had never seen anything like it. It started to float off into the sky red bolts surrounding it it flew up until they couldn't see it anymore. They ran down to to port to find... "Commander. It's Nihlus." He was... dead. He was lying on the ground not moving head covered in blood as if someone shot him from behind.

Then they heard movement, and Shepard took out his pistol, it could've been the person who shot Nihlus. "Somethings moving! Over behind those crates!" Ashley yelled. Then someone - a human man emerged from behind the crates fast with his hands up. "Wait! Don't - Don't shoot! I'm one of you! I'm human." "What are you doing sneaking around back there?" Shepard asks. "I... I'm sorry I was hiding. From those creatures." Shepard decides to put the gun away. "My name's Powell. I saw what happened to that turian. The other one shot him." _'Other one?'_ "I need to know how Nihlus died." "The other one got here first. He was waiting when your friend showed up. He called him Saren. I think they knew each other. You're friend seemed to relax. He let his guard down... and Saren killed him. Shot him right in the back. I'm just lucky he didn't see me behind these crates." " We were told a Prothean beacon was brought to the spaceport. What happened to it?" Powell points in a direction, "It's over on the other platform. Probably where that Saren was headed. He hopped on the cargo train right after he killed your friend. I knew that beacon was trouble. Everything's gone to hell since we found it. First that damn mother ship showed up. Then the attack. They killed everyone! If I hadn't been behind the crates I'd be dead too." Then a question popped into Shepard's mind. "How come you're the only on who survived? Why didn't anyone else try to hide behind the crates?" The man started to look nervous, "They never had a chance. I... I was already behind the crates when the attack started." _'Say what now?"_ Kaidan held a hand up. "Wait a minute. You were hiding behind the crates before the attack?" Powell started to look more nervous. "I... sometimes I need a nap to get through my shift. I sneak behind the crates to grab forty winks to where the supervisor can't find me." That got Ashley ticked off, "You survived because your lazy?" Shepard spoke before she could do or say anything more. "If you hadn't snuck for that nap you'd probably be dead just like all the others." "Yeah. Yeah, I guess. I don't really want to think about it." He answered questions from them about the attack, the beacon, and the mother ship with all of that Shepard decided it was time to go. "We need to find that beacon before it's too late." "Take the cargo train. That's where the other turian went. I... I can't stay here. I need to get away from all this."

They reach the cargo train and use it to get to the other platform. When they get there their presence must have alerted the geth, because they came out guns they got off the platform before Shepard joined the fight he noticed something off to the side. _'Is that... a detonator?'_ "Demolition charges! The geth must have planted them." Kaidan shouted.Immediately Shepard rushed to disarm Ashley figure out what they were trying to do. "Hurry - we need to find them all and shut them down!" By the time he finished Kaidan and Ashley had finished with the geth. "Now we need to find the others! Let's move!" Shepard ordered. They rushed to find the detonators, and they killed any geth that stood in there way. When they were sure they found them all they went down to the beacon to find no one but husks and geth guarding, but they were no problem.

"Normandy, the beacon is secure. Request immediate evac." Kaidan and Ashley stared up at the beacon while Shepard calls for an evacuation. Kaidan speaks in awe, "This is amazing. Actual working Prothean technology. Unbelievable!" The beacon had a green aura swirling around it. "It wasn't doing anything like that when they dug it up," Ashley acknowledged. "Something must have activated it." "Roger, Normandy. Standing by." Shepard said into the comm. Ashley must've been to close to the beacon, because it suddenly started pull her toward it. Shepard noticed it, and ran toward her, and pushed her away towards Kaidan. Suddenly Shepard was pulled up by the beacon and held there. "Shepard!" Ashley yelled trying to reach him in vain, because Kaidan was holding her back. "No! Don't touch him! It's too dangerous!" All Shepard saw were images flashing in and out of his vision before... light... then darkness.

A/N: It took me all day, but I finished! I was just so happy people enjoyed this that I had to post a new chapter, but be warned the other chapters may not come as fast. I'm thanking you guys for actually giving my story a chance and I know it's only been what we've already seen, but like I said this series will be more than, and that fact will be more clear the further we get, but until then my cards are in hand, and out of view. Seriously thank you, thank you so much for giving me a chance. Shout out to the guest that's a Talimancer who left that review and Acedew who said there was no way that this was my first fanfiction, but seriously though it is.


	3. Reminiscing

Anderson says to not think about them too much. It does more harm then good he says.

It may be the one order from Anderson that Shepard never followed, and Anderson knows it. He seemed to be more understanding about Shepard lingering in his past then most people. He also gave the time, space, and support everyone refused to give.

After the raid John Shepard wanted to put all of his anger on all batarians, because any batarian would be easier to find then the slavers who caused his anguish. Although most people ignored him, and just mistaken him for a normal teen who lashed out his problems onto everyone else and will get over it eventually.

However he wasn't a 'normal teen'. He was different then them….in more ways then one. Anderson understood his anger and although he did not share his experience personally he knew one thing. That John didn't need to be treated as a fragile peace of glass or ticking time bomb. He didn't need a psychiatrist or any doctor. He needed a friend who didn't talk to him as if he were a child.

Anderson then sat him down and told him that sometimes things happen and sometimes life doesn't have a reason we could possibly understand. That life will take more than it gives before things get better, and all we can do is not let it get us down, and get back up and push through, for it is in our nature.

Although Anderson preferred Shepard to stay away from his past he knows that it's one of the things that keeps Shepard sane.

Shepard would think about his mother, Hannah Shepard. Her rose red hair she kept out of her face in a bun. Her freckled pale skin with rosy cheeks. The steal blue eyes he himself inherited. Her embraces, her smile, her hands, although calloused from working out in the field, gentle while holding his face. The way she got things done at the farm told you she would've been a great soldier if she hadn't met Johns father.

His father, Caesar Shepard with his hair and stubble, which were both so dark brown they could easily be mistaken for black. His skin more paler than his mothers, and looked as if it never saw light of any kind in his lifetime. If it weren't for his dark yet vibrant green eyes he would look like a black and white portrait. Aside from his ghostly appearance he was beloved and a kind man, and from looking at him you knew he himself would say differently of his own father. Why though, was a story Caesar was not happy telling his son, and one Shepard never like to repeat to this day.

Then there was his younger sister, Jane Shepard. Between to two them she was the renegade, but unlike most she had morale lines she would never cross. Looking back at the picture they had of his mother when she was kid, Jane seemed to have been her spitting image all except for the green eyes she shared with their father. Jane and Johnathan both were different from the other kids. They would not treat each other as nuisances they would hang out together everyday on the field chasing each other or messing with one another. Jane was what John would call a flexible little sneak.

Bottom line the Shepards weren't exactly what people would call normal. There were those talks at night their father would give them to be careful about feeling too much of a single emotion. There was one time their father thought he saw someone while on the field and rushed them all inside. When they got back inside they shut the curtains closed and all of sudden his parents told them to stay in the living room away from the window and to stay quiet. John watched as his parents walked into the kitchen and spoke in hush voices. He couldn't hear any part of the conversation and neither could Jane. They both had to sleep in their parents room that night, he remembered how tightly their parents held them. As if any moment someone would come to take them away.

He missed them.

He missed his family.

Where are they?

A light flashes into view.

He's okay.

He's awake.

A/N: It may seem short and I'm sorry that this took so long, but school started and I had to really focus. Not to mention it's hard to find the right words. I hope this chapter is up to your standards if not there's always next time. I just wanted to bring up his family so badly. They really are an important factor to his story - well of course they are his family. The Raid of Mindoir doesn't seem to affect Shepard in the games and they only seem to mention it a few times, so I thought that Eden Prime and the time he spent blacked out would be a perfect time to squeeze in some personal biz. Fear not I have not forgotten this story it's just nice to make some few nudges before blowing out the whole thing. Hopefully next chapter will not take so long.

P.S. thank you again Acedew or your advice I've taken a note of them I'll be sure to update the 2nd chapter to be much clearer, but I'd like to progress the story a bit first.

Thank you readers. See you next time!


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